98. "Rational design of amyloid binding agents based on the molecular rotor motif" Sutharsan J.; Dakanali, M.; Capule, C. C.; Haidekker, M. A.; Yang, J.; Theodorakis, E. A. ChemMedChem: Chemistry Enabling Drug Discovery, 2009, 5 (1), 56-60

97. "Hexachloroethane: a highly efficient reagent for the synthesis of chlorosilanes from hydrosilanes" Pongkittiphan, Veerachai; Theodorakis, Emmanuel A.; Chavasiri, Warinthorn. Tetrahedron Letters, 2009, 50(36), 5080-5082

96. "Synthesis and anti-HIV activity of conformationally restricted bicyclic hexahydroisobenzofuran nucleoside analogs" Diaz-Rodriguez, Alba; Sanghvi, Yogesh S.; Fernandez, Susana; Schinazi, Raymond F.; Theodorakis, Emmanuel A.; Ferrero, Miguel; Gotor, Vicente Org. Biomol. Chem. 2009, 7, 1415-1423

95. "Evaluation of the pharmacophoric motif of the caged Garciniaxanthones" Chantarasriwong, Oraphin; Cho, Woo Cheal; Batova, Ayse; Chavasiri, Warinthorn; Moore, Curtis; Rheingold, Arnold L.; Theodorakis, Emmanuel A. Org. & Biomol. Chem. 2009, 7, 4886-4894

94. “2,3-tert-butylthiaziridine 1,1-dioxide” Dakanali, M,; Theodorakis, E. A. Encyclopedia of Reagents for Organic Synthesis 2009.

93.  “1,2-bis(tert-butyl)-3-diaziridinone” Dakanali, M,; Theodorakis, E. A. Encyclopedia of Reagents for Organic Synthesis 2009.

92. "Synthesis of 2’,3’-cyclohexene Bicyclic Nucleoside Analogues as Antiviral Compounds" Diaz-Rodriguez, Alba; Fernandez, Susana; Sanghvi, Yohesh S.; Theodorakis, Emmanuel A.; Gotor, Vicente; Ferrero, Miguel. Nucleic Acids Symp. Ser. 2008, 52, 99-100

91. "Characterization of Changes in the Viscosity of Lipid Membranes with the Molecular Rotor FCVJ" Nipper, Matthew E.; Majd, Sheereen; Mayer, Michael; Lee, James, C-M.; Theodorakis, Emmanuel A.; Haidekker, Mark A. Biochim. Biophys. Acta Biomembranes 2008, 1778, 1148-1153.

90. "Studies on the Synthesis of Schisandraceae Natural Products: Exploring A Cyclopropylcarbinol Ring Expansion Strategy" PFischer, Derek; Theodorakis, Emmanuel A. Eur. J. Org. Chem. 2007, 4193-4196.

89. "Selective Activation of Liver X Receptors by Acanthoic Acid-related Diterpenes" Traves, Paqui G.; Hortelano, Sonsoles; Zeini, Miriam; Chao, Ta-Hsiang; Lam, Thanh; Neuteboom, Saskia T.; Theodorakis, Emmanuel A.; Palladino, Michael A.; Castrillo, Antonio; Bosca, Lisardo. Mol. Pharmacol. 2007, 71, 1545-1553.

88. "Molecular Rotors; Fluorescent Biosensors for Viscosity and Flow" Haidekker, Mark A.; Theodorakis, Emmanuel A. Org. & Biomol. Chem. 2007, 5, 1669-1678.

87. "Synthesis and Use of an In-Solution Ratiometric Fluorescent Viscosity Sensor" Fischer, Derek; Theodorakis, Emmanuel A.; Haidekker, Mark A. Nature Protocols 2007, 2, 227-236.

86. "Trifunctional Norrisolide Probes for the Study of Golgi Vesiculation" Guizzunti, Gianni; Brady, Thomas P.; Malhotra, Vivek; Theodorakis, Emmanuel A. Bioorg. & Med. Chem. Lett. 2007, 17, 320-325.

85. "Synthesis and Evaluation of Caged Garcinia Xanthones" Batova, Ayse; Lam, Thanh; Wascholowski, Veit; Yu, Alice L.; Giannis, Athanassios; Theodorakis, Emmanuel A. Org. & Biomol. Chem. 2007, 5, 494-500.

84. "9-borabicyclononyl trifluoromethanesulfonate“ Garvey D. S.; Theodorakis, E. A.; Lee, H. Encyclopedia of Reagents for Organic Synthesis 2006.

83. "Optical Fiber-Based Fluorescent Viscosity Sensor" Haidekker, Mark A.; Akers, Walter J.; Fischer, Derek; Theodorakis, Emmanuel A. Optics Lett. 2006, 31, 2529-2531

82. "Nature-Inspired Approaches to Chemical Synthesis" Sorensen, Erik J.; Theodorakis, Emmanuel A. Tetrahedron 2006, 62, 5169 (Editorial preface).

81. "Chemical Analysis of Norrisolide-Induced Golgi Vesiculation" Guizzunti, Gianni; Brady, Thomas P.; Malhotra, Vivek; Theodorakis Emmanuel A. J. Am. Chem. Soc. 2006, 128, 4190-4191

80. "A Central Strategy for Converting Natural Products into Fluorescent Probes" Alexander, Matthew D.; Burkart, Michael D.; Leonard, Michael S.; Portonovo, Padma; Liang, Bo; Ding, Xiaobin; Joullie, Madeleine M.; Gulledge, Brian M.; Aggen, James B.; Chamberlin, A. Richard; Sandler, Joel; Fenical, William; Cui, Jian; Gharpure, Santosh J.; Polosukhin, Alexei; Zhang, Hal-Ren.; Evans, P. Andrew; Richardson, Adam. D.; Harper, Mary. Kay.; Ireland, Chris M.; Vong, Binh G.; Brady, Thomas P.; Theodorakis, Emmanuel A.; La Clair, James J. ChemBioChem 2006, 7, 409-416

79. "Nitrogen- and Phosphorus-Substituted Benzo-1,4-quinones” in Science of Synthesis, Ed.: A. G. Griesbeck; Lee, H.; Theodorakis, Emmanuel A. Houben-Weyl Methods in Molecular Transformations, Georg Thieme Verlag, Stuttgart, NY, 2006, 28, 71-86 (Book chapter)

78. "Metal-Substituted Benzo-1,4-quinones” in Science of Synthesis" Ed.: A. G. Griesbeck" Vong, Binh G.; Theodorakis, Emmanuel A. Houben-Weyl Methods in Molecular Transformations, Georg Thieme Verlag, Stuttgart, NY, 2006, 28, 13-29 (Book Chapter).

77. "Chalcogen-Substituted Benzo-1,4-quinones” in Science of Synthesis, Ed.: A. G. Griesbeck; Kim, Sun Hee; Theodorakis, Emmanuel A. Houben-Weyl Methods in Molecular Transformations, Georg Thieme Verlag, Stuttgart, NY, 2006, 28, 13-29 (Book Chapter).

76. “A Ratiometric Fluorescent Viscosity Sensor”  Haidekker, M. A.; Brady, T. P.; Lichlyter, D.; Theodorakis, E. A. J. Am. Chem. Soc. 2006, 128, 398-399.

75. "HIF-1alpha expression regulates the bactericidal capacity of phagocytes" Peyssonnaux, Carole; Datta, Vivekanand; Cramer, Thorsten; Doedens, Andrew; Theodorakis, Emmanuel, A.; Gallo, Richard L.; Hurtado-Ziola, Nancy; Nizet, Victor; Johnson, Randall S. J. Clin. Invest. 2005, 115, 1806-1815.

74. "Effects of Solvent Polarity and Solvent Viscosity on the Fluorescent Properties of Molecular Rotors and Related Probes" Haidekker, M. A.; Brady, T. P.; Lichlyter, D.; Theodorakis, E. A. Bioorg. Chem. 2005, 33, 415-425.

73. "Norrisolide: Total Synthesis and Related Studies" Brady, T. P.; Kim, S. H.; Wen, K.; Kim, C.; Theodorakis, E. A. Chemistry Eur. J. 2005, 11, 7175-7190.

72. "Synthetic Studies Towards the Zoanthamine Alkaloids: Synthesis of the Fully Functionalized BC Ring Motif" Rivas, F.; Ghosh, S.; Theodorakis, E. A. Tetrahedron Lett. 2005, 46, 5281-5284.

71. "Synthesis and Evaluation of 6-hydroxy-7-methoxy-4-chromanone- and chroman-2-carboxamides as antioxidants" Lee, H.; Lee, K.; Jung, J.-K.; Cho, J.; Theodorakis, E. A. Bioorg. & Med. Chem. Lett. 2005, 15, 2745-2748.

70. "Sensing of Flow and Shear Stress Using Molecular Rotors" Haidekker, M. A.; Akers, W.; Lichlyter, D.; Brady, T. P.; Theodorakis, E. A. Sensor Lett. 2005, 3, 42-48. 

69. "A New Family of Synthetic Diterpenes that Regulates Cytokine Synthesis by Inhibiting IkB Phosphorylation" Chao, T.-H.; Lam, T.; Vong, B. G.; Traves, P. G.; Hortelano, S.; Chowdhury, C.; Bahjat, F. R.; Lloyd, G. K.; Moldawer, L. L.; Bosca, L.; Palladino, M. A.; Theodorakis, E. A. ChemBioChem 2005, 6, 133-144.